131 dependents
| Package | Description | Downloads/month |
|---|---|---|
| A Swiss-Army-Knife for Bioinformaticians | 31K | |
| A Swiss-Army-Knife for manipulating phylogenetic trees | 17K | |
| Comparative genomics automation and standardization software | 8K | |
| Make a tree from a HAR file | 7K | |
| MetaCHIP2 | 7K | |
| Estimation of BDEISS-CT parameters from phylogenetic trees. | 7K | |
| Fungal Validation and Identification Pipeline | 4K | |
| Ancestral character reconstruction and visualisation for rooted phylogenetic tre... | 3K | |
| Automated modeling and machine learning framework FEDOT | 2K | |
| A python toolkit for single-cell tumor phylogenetic analysis | 2K | |
| The Microbial Co-occurrence Network Explorer | 2K | |
| PhyloDeep is a python library for parameter estimation and model selection from ... | 2K | |
| Python code to generate BEAST2 XML files | 2K | |
| An automated pipeline for high throughput phylodynamic analyses using BEAST 2. | 2K | |
| Accurate, resource-frugal and deterministic DNA sequence classifier. | 2K | |
| Simulation of rooted phylogenetic trees under a given Multi-Type Birth–Death mod... | 2K | |
| Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding dat... | 2K | |
| A tool to analyse Hierarchical Orthologous Groups (HOGs) | 2K | |
| phylogenetic inference of genotype-collapsed trees | 2K | |
| Functional ANnoTAtion based on embedding space SImilArity | 1K | |
| Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding dat... | 1K | |
| Three-item analysis python package | 1K | |
| Pan-Genome Analysis Pipeline | 1K | |
| Microbiome classification pipeline | 1K | |
| FastOMA is a scalable software package to infer orthology relationship. | 1K | |
| A proteomics search engine for LC-MS1 spectra. | 976 | |
| OMAmer - tree-driven and alignment-free protein assignment to sub-families | 966 | |
| sourmash plugin for improved plotting/viz and cluster examination. | 954 | |
| MOB-suite: Software tools for clustering, reconstruction and typing of plasmids ... | 946 | |
| Breakpoint graph implementation in Python programming language | 931 | |
| DeepMicroClass, a deep learning based contig prediction tool | 859 | |
| Metagenomic profiling using a reference phylogeny | 848 | |
| Ancestral sequence reconstruction using a tree structured Ornstein Uhlenbeck var... | 766 | |
| A python library for bioinformatics | 729 | |
| Birth-death epidemiological parameter estimator accounting for partner notificat... | 714 | |
| Variational Inference for Cell Type Evolution | 710 | |
| 701 | ||
| Phylogenetic profiling with orthology data | 692 | |
| library to interact and build OMA hdf5 files | 684 | |
| Segmentation free factor analysis for sub-micron resolution spatial transcriptom... | 677 | |
| SimPhyni: a tool for phylogenetic trait simulation and inference. | 652 | |
| Kssdtree is designed for the construction and visualization of phylogenetic tree... | 646 | |
| Python package to download and filter GenBank database based on taxonomy | 630 | |
| Advanced Pipeline for Simple yet Comprehensive AnaLysEs of DNA metabarcoding dat... | 628 | |
| BABAPPAi: diagnostic framework for identifiability of episodic branch-site struc... | 626 | |
| Pandoo: a pipeline of tools for bacterial genomics. | 596 | |
| Web interface of GrapeTree, which is a program for phylogenetic analysis. | 574 | |
| Check eukaryotic genomes or MAGs for completeness and contamination | 570 | |
| A phylogenetic and geographic analysis tool | 562 | |
| Python library for mutational spectra analysis | 559 |
